From 0baaf60f1975896d048056ca9c137e3c0036c43b Mon Sep 17 00:00:00 2001 From: Peter Cock Date: Thu, 28 Mar 2024 20:26:20 +0000 Subject: [PATCH 1/2] Try increasing the SeqXML parser block size Hopefully this will fix #4640. If it does, this is due to CPython issue 115133 and is a side effect of a CVE security fix. --- Bio/SeqIO/SeqXmlIO.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Bio/SeqIO/SeqXmlIO.py b/Bio/SeqIO/SeqXmlIO.py index 4b95491c4c8..6310adbf0bc 100644 --- a/Bio/SeqIO/SeqXmlIO.py +++ b/Bio/SeqIO/SeqXmlIO.py @@ -441,7 +441,8 @@ class SeqXmlIterator(SequenceIterator): method calls. """ - BLOCK = 1024 + # Small block size can be a problem with libexpat 2.6.0 onwards: + BLOCK = 2048 def __init__(self, stream_or_path, namespace=None): """Create the object and initialize the XML parser.""" From 7da67678299b5cc8d41fa1d667eb5054f1c13f4a Mon Sep 17 00:00:00 2001 From: Peter Cock Date: Fri, 29 Mar 2024 12:02:48 +0000 Subject: [PATCH 2/2] Double it again to 4k See discussion on #4640 --- Bio/SeqIO/SeqXmlIO.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Bio/SeqIO/SeqXmlIO.py b/Bio/SeqIO/SeqXmlIO.py index 6310adbf0bc..8fe75ebb728 100644 --- a/Bio/SeqIO/SeqXmlIO.py +++ b/Bio/SeqIO/SeqXmlIO.py @@ -442,7 +442,7 @@ class SeqXmlIterator(SequenceIterator): """ # Small block size can be a problem with libexpat 2.6.0 onwards: - BLOCK = 2048 + BLOCK = 4096 def __init__(self, stream_or_path, namespace=None): """Create the object and initialize the XML parser."""